Friday, February 19, 2010

A Two-For-One Absurdity: Junk DNA Meets Evolvability

Tandem repeats are short stretches of DNA that are repeated head-to-tail. "At first sight," explains evolutionist Marcelo Vinces, "it may seem unlikely that this stutter-DNA has any biological function." This is an example of how evolutionary thinking harms science. Since life is an accident, biology must be straightforward. If we do not immediately perceive how something works, then evolutionists typically think it is non functional junk. Over and over this evolutionary expectation has turned out wrong. And now again with tandem repeats:

unstable junk DNA allows fast shifts in gene activity, which may allow organisms to tune the activity of genes to match changing environments--a vital principle for survival in the endless evolutionary race.

The tandem repeats allow for swift adaptation to environmental demands, so cells with more repeats stand a better chance. As the evolutionists explain, "Their junk DNA saved their lives."

Of course none of this is impossible. But it calls for a healthy dose of serendipity. We are now to believe that evolution created these DNA sequence patterns which were useless for generations. Nonetheless evolution maintained them in the population. That was fortunate because one day, when the environment presented new challenges, they saved the day.

Or there is the preadaptation explanation. It holds that there are some previous functions that the design performed. Like Darwin's gardener we can't observe them anymore, but we can hypothesize.

Either way the result is that evolution created more evolution. Evolutionists now routinely speak of the evolution of evolvability. In other words, we must believe that evolution created the ability to evolve.

Impossible? Certainly not.

The obvious scientific conclusion? You've got to be kidding.

An undeniable fact? I have a bridge to sell you.

But evolutionists do mandate that it is a fact. And therefore they must conclude that what they thought was junk DNA has now saved the day. Evolutionists are flipping between absurdities in what is increasingly looking like a parody. The evolution literature looks more and more like a spoof. As if sensing the problem, the science writer reporting on the new research hastened to add that it is to be published in a reputable journal.

Dr Hunter, I enjoy your updates on evolutionary science. I had missed the Vinces et al. paper in Science.

A question: You said, "We are now to believe that evolution created these DNA sequence patterns which were useless for generations." What led you to think that those sequences had been useless at some time in the past? I didn't see anything in the paper that commented on the history of those sequences.

"This is an example of how evolutionary thinking harms science. Since life is an accident, biology must be straightforward."

Absolutely not. Whoever said that? Why must life be straight-forward if it is the product of blind forces making hapzard, kludgey improvements piece by piece?

"If we do not immediately perceive how something works, then evolutionists typically think it is non functional junk."

As opposed to ID, which typically think it is evidence for supernatural tinkering?

If we do not immediately perceive how something works, what ELSE are we to think of it other than non-functional junk? This seems to be a pretty sensible default assumprion until we can find out what it does.

"Over and over this evolutionary expectation has turned out wrong."

So basically, in other words, 'over and over again, we have discovered the function of what we previously thought was non-function junk DNA?' Ummm, why is this a surprise? Or how does it undermine evolution? We research stuff and find things out. That is normal. It is what scientists do.

"Of course none of this is impossible. But it calls for a healthy dose of serendipity."

Do you have a more likely alternative to propose?

"We are now to believe that evolution created these DNA sequence patterns which were useless for generations."

Okay, stop me if I'm wrong but isn't junk DNA just remnant DNA - genes which were useful to the animal's ancestors but are no longer used? For example, the genes for eyes in species who have lost their eyes, such as blind cave salamanders.

"So basically, in other words, 'over and over again, we have discovered the function of what we previously thought was non-function junk DNA?' Ummm, why is this a surprise? Or how does it undermine evolution? We research stuff and find things out. That is normal. It is what scientists do."

One of the marks of science is that it makes predictions. Presumably, if the prediction fails, the hypothesis under investigation has been falsified. Or has it?

It may be that the hypothesis was formulated based on an incomplete understanding of the phenomenon under investigation. So the fact that the prediction failed leads science to develop a new more refined hypothesis.

The question then becomes at what point does science abandon a hypothesis (and its "offspring") if prediction after prediction fails?

It seems that evolutionary science will continue on forever with failed prediction after failed prediction. If evolutionary science continues to ignore failed predictions, then what?

I recognize that there is no pat answer to this question, but there has to be a message somewhere in the pile of failed predictions.

It is not the case that the theory of evolution itself relies on any particular gene or set of genes being 'junk' which has then show to have a function.

If this was the case, you would indeed be right.

The truth is more vague than that. Junk DNA is something we would well expect if the theory of evolution was true. And we do indeed find much of it.

However, we do tend to classify any gene sequence we cannot find a function for as 'junk'. This is because we cannot find a function for it. If we then later find a function for it, we discover it is not really 'junk' at all.

But this does not undermine the theory of evolution. It just means we have found a function for genes which we thought did not have one.

Do you see the shameless spin which has been put on this?

Evolution accounts for the gene sequences we deem functionless junk. And the fact that occassionally certain gene sequences are pulled from the rubble and shown not to actually be junk at all does not undermine this fact. Nor does it undermine the fact that ID does NOT account for this 'junk'. Which is the more relevant point when comparing the two theories.

To further clarify the reasoning process, I pose a hypothetical question.

You say that the theory of evolution expects to find junk DNA. As long and as tedious as the process might be, what would be the conclusion offered up if every instance of purported junk DNA turned out to have function?

Well I'll be honest, if ALL junk DNA was found to have a function, I suppose my first reaction would be to look for a mechanism which deletes gene sequences as soon as they become obsolete. Though I have no idea what that mechanism might be.

I'm sure this sounds like I'm demonstrating your point for you. If you think so, let me reiterate that finding a function for gene sequences we previously thought were functionless 'junk' does not count as a failed prediction. It would only do so if the theory of evolution specified CERTAIN SPECIFIC genes sequences as junk (which then turned out to have a function), which it does not. Instead, it merely accounts for the large amounts of junk DNA we do, in fact, find.

Also, we cannot simply divide gene sequences neatly into 'those we have identified a function for' and 'those we have not identified a function for and therefore assume to be junk'. There are many genes sequences which are 'broken' or for some reason not expressed in the host creature. I used the example earlier of gene sequences for eyes in blind cave salamanders (who have lost their eyes). Why should they carry gene sequences for making eyes (albeit 'broken' ones)? The theory of evolution provides an answer - they are descended from creatures who had functioning eyes.

Such 'broken' gene sequences will deteriorate and break up over time, and will eventually be lost in the background 'white noise' of junk DNA (which, to my knowledge, is what junk DNA is really made up of).

Nor is this a rare and strange anomaly - we find all sorts of such sequences in the genes of all sorts of animals. The whole evolutionary history of an animal is written in its DNA. As Sean B. Carroll puts it in his book The Making Of The Fittest: "Every evolutionary change between species, from physical form to digestive metabolism, is due to - and recorded in - changes in DNA. So, too, is the "paternity" of species. DNA contains, therefore, the ultimate forensic record of evolution." (P.14)

So let me ask you - how should we consider gene sequences such as those for making eyes in blind cave salamanders? They are functionless in that they are not expressed in the animal itself. Yet their function is not a mystery to us because we know what they WERE used for. So it's not like someone tomorrow is going to suddenly discover their function.

Let me try to summarize what I think I am learning from our very interesting discussion.

There are genes that

1. Have known functions;2. Have previously known functions and are now useless (the blind cave fish example);3. Have unknown functions a. Whose functions may eventually be found. b. Whose functions may “never” be found.

3b is problematic from the standpoint that a gene’s function may be so obscure that even though science hasn’t found its function, a function does exist. This is really a special case of 3a. Can science ever really be sure the there is truly a functionless gene (that is not a “decayed” gene)?

ID predicts that functions for junk DNA will be found. ID also accepts that the “designs” in nature are subject to natural decay, so the “blind cave fish” does not refute the ID hypothesis.

I have reached a point in my thinking where I am not sure that junk DNA sequences are really helpful as a demarcation argument between design and evolution. What would a truly functionless gene sequence mean? Why would natural selection or the intelligent designer create a functionless gene sequence?

And if all genes are found to have function both ID and evolution will claim credit.

"ID predicts that functions for junk DNA will be found. ID also accepts that the “designs” in nature are subject to natural decay, so the “blind cave fish” does not refute the ID hypothesis."

Neither of these statements are quite true. An ID believer may certainly believe these statements, but they are not necessarily entailed by ID. There is no reason why the designer would not include "junk" DNA in his designs; to assert otherwise would be to ascribe characteristics to the designer--such as frugality or parsimony--which ID as a movement generally refuses to do. (Accepting that ID makes statements about the nature of the designer opens the position up to "bad design" arguments.)

Nor does ID require that the "design" is amenable to any sort of decay. Doing so requires asserting that design is something that happened in the past, as opposed to an ongoing process. This, again, is outside the self-imposed bounds of the ID movement, which can no more afford to make statements about the mechanism of design than it can about the nature of the designer.

"Why would natural selection or the intelligent designer create a functionless gene sequence?"

Natural selection wouldn't "create" such a sequence, but it might preserve a functionless sequence created by mutations if the carrying cost of that sequence was low enough. You might also consider genetic drift or other non-selective evolutionary mechanisms. The intelligent designer could create anything, for any reason or no reason. The inability of ID to explain anything is one reason why it isn't science.

"And if all genes are found to have function both ID and evolution will claim credit."

But it would be the scientists who found the functions that would deserve the credit. And it's safe to say that those scientists, like all productive researchers, would not be creationists.

====A question: You said, "We are now to believe that evolution created these DNA sequence patterns which were useless for generations." What led you to think that those sequences had been useless at some time in the past? I didn't see anything in the paper that commented on the history of those sequences.====

Imagine a truly vast surface covered in bricks and rubble. Occasionally, here and there, buildings stand. But some of these buildings are in disarray and in various states of ruin. But at what point do collapsing ruins cease to be collapsing ruins, and simply become part of the surrounding rubble?

I trust the metaphor is clear enough. But to hammer it home, trying to distinguish between deteriorating gene sequences and junk DNA is like distinguishing between a collapsing building and the rubble.

As far as I know, all junk DNA was once part of a functioning gene sequence (a point which is not obvious from my metaphor, but still...). It all used to have a function in some sequence or other. But in most cases these sequences have deteriorated beyond identification. I admit I am not rock solidly confident on this point, but that is my understanding of it, anyway.

"I have reached a point in my thinking where I am not sure that junk DNA sequences are really helpful as a demarcation argument between design and evolution."

I believe the relevant point is that evolution accounts for junk DNA while ID does not. Sequences such as deteriorating eye sequences in blind cave fish are exactly what we should expect to find if they really were descended from fish with functioning eyes. This is not absolute proof - the sequence may just happen to exist by chance. But that is exceedingly unlikely. Yet the theory of evolution predicts the existence of such 'unlikely' sequences. A prediction which is validated over and over again for every such sequence we identify.

Moreover, even taken at face falue, junk DNA is the sort of thing we should expect if genes built and arranged themselves blindly. Decaying sequences seem to imply a lack of forethought and design. I know we cannot assume to know the mind of such an intelligent creator (Cornelius, for one, would have my guts for garters if I did), but, like 'badly designed' features, it is another curious fact which seems to go against the hypothesis of nature having been designed.

ID, as Learned Hand points out, does not account for junk DNA - well, any more than it accounts for anything at all. If we are to make no judgements of such a designer, on what it would or would not design, then ID does not predict ANY particular state of affairs over another. Not junk DNA's existence over it's non-existence, not any particular pattern in the fossil record over any other, not any particular distribution of animal species - nothing.

ID makes no predictions at all, in fact, and for this reason (and others), simply fails to be a scientific theory.

I suggest you break your car, stick it in a auto-mechanics shop and then hope that "blind forces making hapzard, kludgey improvements piece by piece" will fix it.

"Oh but that isn't biology or life", you will say. Indeed, what IS life?

In the end it doesn't even matter, for all the data and the math are against you and you will always lose these bio-lotteries because blind, purposeless nature isn't trying to fix, let alone make, anything at all.

"As opposed to ID, which typically think it is evidence for supernatural tinkering?"Let me see, how many times has this erroneous statement been defeated here?

Do you ever learn anything?!? Of course not, how can you when your mind is obviously on hold.

Thats another thing one must admire in Darwinians - their persistence in repeating as true previosly exposed error.

You're very good at this. Unfortunately for you, as long as ID is not about the supernatural, you will always be wrong.

As I suggested before you seriously need to go back to school and learn critical thinking and reason.

"ID makes no predictions at all, in fact, and for this reason (and others), simply fails to be a scientific theory."

The only reasonable reaction to such a glaringly false statement is ROTFLMAO!!

...Or perhaps tears of sadness for witnessing such impoverished and ignorant thinking.

"When Darwin presented a paper [with Alfred Wallace] to the Linnean Society in 1858, a Professor Haugton of Dublin remarked, `All that was new was false, and what was true was old.' This, we think, will be the final verdict on the matter, the epitaph on Darwinism." -Fred Hoyle and N. Chandra Wickramasinghe, Evolution from Space (1981), p. 159.

That is the simple truth of it.

As for ID predictions, here is a short summary view:1. Ways Designers Act When Designing (Observations):- Take many parts and arrange them in highly specified and complex patterns which perform a specific function.- Rapidly infuse any amounts of genetic information into the biosphere, including large amounts, such that at times rapid morphological or genetic changes could occur in populations.- 'Re-use parts' over-and-over in different types of organisms (design upon a common blueprint).- Be said to typically NOT create completely functionless objects or parts (although we may sometimes think something is functionless, but not realize its true function).

Therefore:2. Some Predictions of Design (Hypothesis):- High prescriptive information content - Machine-like irreducibly complex structures will be found- Forms will be found in the fossil record that appear suddenly and without any precursors- Genes and functional parts will be re-used in different unrelated organisms- The genetic code will NOT contain much discarded genetic baggage code or functionless "junk DNA"- Few intermediate forms will found giving a clear and gradual pathway from one family to another - there are none so far * Most of the claimed ancestors will be shown to have serious problems - already historically proven - mechanisms for error detection and correction will be abundant within bio organisms- mechanisms for *non-random* cellular adapatations coherent with environmental pressures will be found- So called vestigial organs will be found to have specific purpose and usefulness - proven- ...

But your problem is far deeper than you are able to realize.

"A scientific theory is an established and experimentally verified fact or collection of facts about the world. Unlike the everyday use of the word theory, it is not an unproved idea, or just some theoretical speculation. The latter meaning of a 'theory' in science is called a hypothesis. -http://www.whatislife.com/glossary/t.htm

Now compare the above definition of 'theory' to the following:

"The history of organic life is undemonstrable; we cannot prove a whole lot in evolutionary biology, and our findings will always be hypothesis. There is one true evolutionary history of life, and whether we will actually ever know it is not likely. Most importantly, we have to think about questioning underlying assumptions, whether we are dealing with molecules or anything else." Jeffrey H. Schwartz, Professor of Biological Anthropology, University of Pittsburgh, February 9, 2007

Darwinism is so inundated with specualtive hypotheses that it doesn't really even qualify as valid theory!

Most of Darwinism predictions on the contrary, have failed over and over again as Dr. Hunter points out.Still I suspect this, as usual, will mean nothing to you since you are stuck in the materialist holding pattern, can't navigate your way out and you are running out of fuel.

"As I suggested before you seriously need to go back to school and learn critical thinking and reason."

This is a mildly ironic comment, coming as it does at the end of a block of angry but empty rhetoric. Let us pause also and observe that the schools that teach "critical thinking and reason" also teach evolutionary biology. To learn creationism, one must go to a school such as BIOLA that starts with a doctrinal statement of faith and teaches to the ideology.

Hitch claims: "Unfortunately for you, as long as ID is not about the supernatural, you will always be wrong.

It sounds like you are saying - for yourself, at least - that God is not likely to be the designer.

Or perhaps you mean to say that ID can't distinguish between a natural and a supernatural agent.

"2. Some Predictions of Design (Hypothesis):- High prescriptive information contentPerhaps, but this is not much different from the predictions of neoDarwinists. The junk DNA hypothesis has never been well supported by neoDarwinists, incidentally, although it is not clear from your use of Darwinism the extent to which you distinguish between different lines of evolutionary thought.

- Machine-like irreducibly complex structures will be found Predicted, originally, by Muller in 1918 under natural selection. Not a unique claim to ID, except that the term "irreducible complexity" is novel and misleading.

- Forms will be found in the fossil record that appear suddenly and without any precursorsThe fossil record is biased and imperfect and records a geologic and not evolutionary timescale. It is unsurprising that there is not seamless morphological transition.

When I say biased, I mean that the fossil record largely only holds the history of hard structures, not whole organisms, and obviously not the underlying genetic histories of species. Despite this, the fossil record still has a large evidence base of transitional fossils, although ID advocates and YECs seem not to accept this.

We might ask: what genetic changes are likely to underlie body plan changes that could be recorded in the fossil record. Would they be gradual or sudden on a geologic timescale?

- Genes and functional parts will be re-used in different unrelated organismsThis is primarily the prediction of common descent under naturalistic evolution, except for the use of the term "unrelated". What do you mean by unrelated? Actually, which organisms are unrelated, and what is your basis for saying so? Because the prediction under common descent is that homologous structures are shared, leading to patterns of nested relatedness between species and higher taxa. This is the pattern that we see in biology.

- The genetic code will NOT contain much discarded genetic baggage code or functionless "junk DNA"How much? Again, most hardline Darwinists already argue in favour of this and always have, against the views of neutralists, who emphasise population-genetic processes involving substantial junk.

- Few intermediate forms will found giving a clear and gradual pathway from one family to another Intermediate forms in the fossil record, you mean? Because certainly if you look at extant taxa, there is a very strong pattern.

- there are none so farThat would be news to paleontologists everywhere.

* Most of the claimed ancestors will be shown to have serious problems - already historically provenSome of this has been overblown claims and wishful thinking from those who have found fossils but - seriously - there is still a substantial fossil record in the relatively recent human lineage, and many other lineages.

- mechanisms for error detection and correction will be abundant within bio organismsOf course they are.

- mechanisms for *non-random* cellular adapatations coherent with environmental pressures will be foundNon-random - the burden of proof would be on you there to demonstrate non-randomness at the molecular level. That is pretty fanciful stuff.

- So called vestigial organs will be found to have specific purpose and usefulness - proven- ..."Indeed many do have purposes. Truly vestigial organs/structures have reduced purposes however. This is the general claim regarding vestigial strcutures, not that they are without function. The prediction of Darwinists would be that such structures, lacking any purpose at all, will disappear over the long-term.

I'm hearing a lot of ranting and bravado, but not many actualy points to counter. While I'm sure telling me how lost and confused I am in a haze of Darwinian thinking is entertaining for you, there's not much there I can actually address, is there?

The one thing of any real substance in your post is the vaccous and wildly inaccurate list of points you present as predictions ID makes, but I see abimer has done a good job of addressing them for me.

So let me add just one final point - these predictions are based on what you think is reasonable to assert a typical designer would do when designing his creation. You are ASSUMING that an intelligent designer would, for example, create a high prescriptive information content, or would not create functionless features. But you have no reason to make these claims. Maybe an intelligent designer would chose to do the opposite of all these things you have predicted, for reasons of their own.

In fact, the way I understand it (and I am not claiming that I truly understand everything he is saying), one of the reasons Cornelius Hunter insists evolution is metaphysical is because it is based on assumptions on what we may or may not expect if biology was designed. He is wrong that evolution does this. But he is right that such assumptions are metaphysical. However, YOU are making these assumptions.

Let's say there is an intelligent designer and it is God, just for argument's sake. You cannot say 'God would not create functionless junk DNA'. He might do just that. For reasons beyond us. So neither the presence or absense of junk DNA is really evidence for design, is it?

I'm never taking out the garbage again. Imagine what it will become, if I let natural selection take it over for me? Junk? What junk? Poof! It's magic...It will be selected for its (name hidden quality that is required by future), and voila!

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/